Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery

Background: Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers t...

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Autores principales:	Rivarola, Maximo Lisandro, Fernández, Paula Virginia, Acuña, Cintia Vanesa, Hopp, Horacio Esteban, Marcucci Poltri, Susana N.
Publicado:	2012
Materias:	de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Nothofagus Nothofagus alpina
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712164_v13_n1_p_Torales http://hdl.handle.net/20.500.12110/paper_14712164_v13_n1_p_Torales
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_14712164_v13_n1_p_Torales
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spelling	paper:paper_14712164_v13_n1_p_Torales2023-06-08T16:17:14Z Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery Rivarola, Maximo Lisandro Fernández, Paula Virginia Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N. de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa Background: Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described.Results: Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic.Conclusions: This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. © 2012 Torales et al.; licensee BioMed Central Ltd. Fil:Rivarola, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Fernández, P. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Acuña, C.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Hopp, H.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Poltri, S.N.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2012 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712164_v13_n1_p_Torales http://hdl.handle.net/20.500.12110/paper_14712164_v13_n1_p_Torales
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa
spellingShingle	de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa Rivarola, Maximo Lisandro Fernández, Paula Virginia Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N. Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
topic_facet	de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa
description	Background: Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described.Results: Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic.Conclusions: This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. © 2012 Torales et al.; licensee BioMed Central Ltd.
author	Rivarola, Maximo Lisandro Fernández, Paula Virginia Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N.
author_facet	Rivarola, Maximo Lisandro Fernández, Paula Virginia Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N.
author_sort	Rivarola, Maximo Lisandro
title	Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
title_short	Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
title_full	Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
title_fullStr	Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
title_full_unstemmed	Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
title_sort	transcriptome survey of patagonian southern beech nothofagus nervosa (= n. alpina): assembly, annotation and molecular marker discovery
publishDate	2012
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712164_v13_n1_p_Torales http://hdl.handle.net/20.500.12110/paper_14712164_v13_n1_p_Torales
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_version_	1768546644023836672

Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery

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